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v v CL E s 0 0 0 0 0 15 0 U HISTORICAL DNA REVEALS EXTINCTIONS AND INVASIONS 9 �n AA -,4-,- ARAN \ /A 1— .4.- .:.. --- 0 14 20 30 40 50 6a 70 80 90 100 % sequence variation by drainage Southern Rocky Mountains. Our phylogenetic survey of fish collected prior to the onset of extensive propa- gation and stocking of fish revealed six divergent lin- eages, not four as originally described by 19 and 20th century fish taxonomists (1-11). Each cutthroat lineage was probably endemic to either a single drain- age basin or two adjacent drainage basins, but the native distribution of subspecies probably differs from the prevailing view in several ways (1-12). Notably, instead of the expected one, there were three distinct lineages historically native to the drainage basins on the western slope of the Continental Divide. Further- more, the subspecies native to the South Platte was probably endemic to the drainage basin, and not a native of the Arkansas River drainage as originally described. Additionally, museum specimens identified as Oncorhynchus clarkii macdonaldi were found in the Arkansas drainage as expected, but not just to a pair of headwater lakes as originally described (Jordan 1891). The distribution of O. c. virginalis aligned with the prevailing view and was only detected in the Rio Grande River drainage basin. Our third hypothesis could not be refuted. We discovered that the current and historical distribution of cutthroat trout lineages were significantly different. The difference probably reflects the success of past fish propagation and stock- ing activities, which broadly distributed two lineages of cutthroat trout that were historically native to waters west of the Continental Divide. The decline from six lineages in the museum samples to four today suggests there were two extinction events: one in the Arkansas River basin and another in the San Juan River system. Importantly, we discovered that the cutthroat lineage historically native to the South Platte, that at one time was declared extinct, persists in a single stream outside its native range. © 2012 Blackwell Publishing Ltd Fig. 6 AMOVA analysis by drainage. The modern sequence data set was subsam- pled so that the number of samples from each drainage basin matches the sample size of the museum data set. The per cent sequence variation explained by drainage for 1000 subsampled modern data sets is shown as a histogram in black (95 % of values) and grey (5 % tail of values). The per cent variation explained by drainage for museum sam- ples is indicated with an arrow. The role of stocking in the contemporary distribution of Colorado's cutthroat trout AMOVA results support the hypothesis that stocking has radically changed the geographical distribution of cut- throat trout lineages in Colorado. Discordance between the historical and modern distribution of diversity is best explained by the widespread stocking of cutthroat trout across the state of Colorado. More specifically, stocking activities spanning 1899 -1931 from the Grand Mesa Lakes within the Gunnison Basin and from 1903- 1938 from Trappers and Marvine Lakes in the headwa- ters of the White River within the Yampa basin may explain why the two lineages native to these drainages are abundant in high elevation streams across major drainage basins on both slopes of the Continental Divide (Fig. 7). Importantly, many trout were stocked into historically fishless waters above barriers. Follow- ing the founding stocking events, those same barriers have protected these populations from non - native sal - monids such as brook, brown (Salmo trutta) and rain- bow trout that tend to replace or hybridize with native cutthroat trout (McGrath & Lewis 2007, Metcalf et al. 2008; Peterson et al. 2008; Bennett et al. 2010; Benjamin et al. 2011). The end result is a patchwork of cutthroat trout lineages that persist in small, high elevation popu- lations across the state of Colorado. In addition to stocking by federal and state agencies, stocking activities by private fish culturists that began in the late 19th century also appears to have played a role in the distribution of cutthroat trout in Colorado. Exhaustive surveys of contemporary populations within the South Platte basin have failed to find the clade char- acterized in museum specimens as native to the South Platte River. Instead, we discovered the trout native to the South Platte persists in an approximately four -mile